Entering W2 Box W - Employer contributions to Health Savings Account is generating taxable income

I've already entered business income (from my rentals and my wife's consulting) and am now entering my W2 information in the Personal section.  When I enter the information for box "W - Employer contributions to Health Savings Account" from my employer provided W2 ($2,139.65), it's causing my Federal Refund to go down.  Why is this happening?  I have  a high deductible health care plan, and my understanding is that contributions to my HSA (which I technically made, not my employer, even though the box is labeled as such), are pre-tax and not taxable.  Shouldn't my Federal Refund go UP, not down?